//virtual bool datafile::getSpectrum( int fcn, size_t pos, adcontrols::MassSpectrum& ms, uint32_t objId ) const { (void)fcn; try { EDAL::IMSSpectrumCollectionPtr pSpectra = pAnalysis_->GetMSSpectrumCollection(); EDAL::IMSSpectrumPtr pSpectrum = pSpectra->GetItem( long(pos) + 1 ); // 1-origin if ( pSpectrum->Polarity == EDAL::SpectrumPolarity::IonPolarity_Negative ) ms.setPolarity( adcontrols::MS_POLARITY::PolarityNegative ); else if ( pSpectrum->Polarity == EDAL::SpectrumPolarity::IonPolarity_Positive ) ms.setPolarity( adcontrols::MS_POLARITY::PolarityPositive ); else ms.setPolarity( adcontrols::MS_POLARITY::PolarityIndeterminate ); adcontrols::MSProperty prop = ms.getMSProperty(); prop.setTimeSinceInjection( static_cast< unsigned long >( pSpectrum->RetentionTime /* sec */ * 1.0e6 ) ); // usec ms.setMSProperty( prop ); // <- end of prop set _variant_t vMasses, vIntens; if ( objId <= 1 ) { pSpectrum->GetMassIntensityValues( EDAL::SpectrumType_Profile, &vMasses, &vIntens ); ms.setCentroid( adcontrols::CentroidNone ); // profile } else { // objId should be 2 pSpectrum->GetMassIntensityValues( EDAL::SpectrumType_Line, &vMasses, &vIntens ); ms.setCentroid( adcontrols::CentroidNative ); } SafeArray sa_masses( vMasses ); ms.resize( sa_masses.size() ); ms.setMassArray( reinterpret_cast< const double *>( sa_masses.p() ) ); SafeArray sa_intensities( vIntens ); ms.setIntensityArray( reinterpret_cast< const double *>( sa_intensities.p() ) ); ms.setAcquisitionMassRange( ms.getMass( 0 ), ms.getMass( ms.size() - 1 ) ); return true; } catch(_com_error& ex ) { ADERROR() << std::wstring( ex.ErrorMessage() ); return false; } return false; }
bool waveform::fft::lowpass_filter( adcontrols::MassSpectrum& ms, double freq ) { if ( ms.isCentroid() ) return false; size_t totalSize = ms.size(); (void)totalSize; size_t N = 32; while ( N < ms.size() ) N *= 2; const size_t NN = ms.size(); double sampInterval = ms.getMSProperty().getSamplingInfo().fSampInterval(); // seconds if ( sampInterval == 0 ) sampInterval = ( ms.getTime( ms.size() - 1 ) - ms.getTime( 0 ) ) / ms.size(); const double T = N * sampInterval; // time full scale in seconds. Freq = n/T (Hz) // power spectrum has N/2 points and is n/T Hz horizontal axis := data[N/2] = (N/2)/T Hz size_t cutoff = size_t( T * freq ); adportable::array_wrapper<const double> pIntens( ms.getIntensityArray(), N ); std::vector< std::complex<double> > spc( N ); std::vector< std::complex<double> > fft( N ); size_t n; for ( n = 0; n < N && n < NN; ++n ) spc[ n ] = std::complex<double>( pIntens[ n ] ); while ( n < N ) spc[ n++ ] = pIntens[ NN - 1 ]; adportable::fft::fourier_transform( fft, spc, false ); // appodization for ( size_t i = cutoff; i < N - cutoff; ++i ) fft[ i ] = 0; //adportable::fft::apodization( N/2 - N/16, N / 16, fft ); adportable::fft::fourier_transform( spc, fft, true ); std::vector<double> data( N ); for ( size_t i = 0; i < NN; ++i ) data[ i ] = spc[i].real(); ms.setIntensityArray( &data[0] ); return true; }
//virtual bool datafile::getSpectrum( int /* fcn*/, size_t idx, adcontrols::MassSpectrum& ms, uint32_t /* objid */) const { if ( lrpfile_ && unsigned( idx ) < lrpfile_->number_of_spectra() ) { if ( auto msdata = (*lrpfile_)[ idx ] ) { std::vector< double > time, intens; if ( lrpfile_->getMS( *msdata, time, intens ) ) { ms.resize( time.size() ); ms.setMassArray( time.data() ); ms.setIntensityArray( intens.data() ); ms.setAcquisitionMassRange( time.front(), time.back() ); return true; } } } return false; }